Chapter 4: 4.4 Characteristics of Membrane Proteins Flashcards
What are the two types of proteins in the lipid bilayer?
- Peripheral
- Integral
Define:
Glycoproteins
Proteins with lipid post-translational modifications that aid in membrane insertion and cell recognition
What are the two types of integral proteins?
- Transmembrane
- Monotopic
List:
Ways peripheral membrane proteins can be attached to the membrane
- Amphipathic helices
- Hydrophobic loop regions
- Attachment to integral proteins
- Ionic and H-bonds
What are the methods to remove peripheral membrane proteins?
- High salt method
- pH change
Describe:
Removal of Peripheral Membrane Proteins via High salt method
- Neutralizes or “shields” charges using ions in salt
- Breaks hydrogen bonds and ionic interactions
Describes:
Removal of Peripheral Membrane Proteins via pH change
- Protonates/deprotonates charged amino acids
- Breaks hydrogen bonds and ionic interactions
Define:
Integral Membrane Proteins
Completely span the membrane
How many types of integral membrane proteins are there?
6
Describe:
Each type of integral membrane proteins
- Type I: Single pass amino group (NH3+) on outside
- Type II: Single pass amino group (NH3+) on inside
- Type III: Single protein with multiple passes
- Type IV: Multiple proteins each with single passes
- Type V: Held to membrane via lipid anchor
- Type VI: Held to membrane via trans-membrane segment and lipid anchor
What are the regions of the cellular membrane?
- Extracellular-facing region
- Membrane spanning regions
- Intracellular-facing region
State:
Purpose of Extracellular-facing region
Play roles in signalling, transport, and cell recognition and communication (Lipids and glycosylated proteins)
State:
Purpose of Membrane spanning regions
~20 amino acids long and mostly hydrophobic
State:
Purpose of Intracellular-facing region
Transmit signals to the cytosol through “tails” and are involved in transport
How are integral membrane proteins removed?
Requires harsh removal (detergents or organic solvents)
* Detergents separate proteins from lipids
How is amino acid hydrophobicity measured?
- Partitioning method
- Surface exposure
In the partitioning method:
How is amino acid hydrophobicity measured?
Observe amino acid distribution between organic solvent (non-polar) and aqueous solvents (polar)
In the partitioning method:
What are two solvents used to mimic conditions for the partitioning methods?
- n-octanol (non-polar): Close to conditions of membrane interior
- Water (polar): Close to conditions of cytosol
State:
The formula for partition coefficient
P(AA) = C(AA nonpolar) / C(AA polar)
True or False:
The partition coefficient is reported as the formula
Not exactly, often reported as log of this value
Are polar or non-polar amino acids found on the surface of proteins?
Polar
Are polar or non-polar amino acids found in the interior of proteins?
Non-polar
The average accessibility of each amino acid is determined by…
From the coordinates of 12 model globular proteins
What is hyrdropathy calculated as in surface exposure?
As the fraction of the total number of the protein that is at least 95% buried from the surface
Describe:
The process of Assigning Transmembrane Sequences based on Hydropathy
- Assign hydropathy value to each residue in the protein (either a positive or negative value) - using Kyte-Doolittle Hydropathy scale
- In a series of 7 residues the average of the seven values is assigned to amino acid in position 4
- Move over one residue and perform calculation
- Plot on grid
What is a problem when trying to span the non-polar membrane?
The polar backbone
How is a non-polar membrane spanned?
Typically form alpha-helix 20-25 amino acids long to span 3-4 nm membrane
True or False:
100% of single spanning proteins utilize the alpha-helix
True
Besides the polar backbond in a non-polar membrane, what is another issue in membrane protein folding?
The fact that most hydrophobic residues have a higher propernsity to form beta-sheets
Hydrophobic resides having a higher propensity to form beta sheets is based on…
Chou-Fasman parameters
Due to hydrophobic residues:
The need to neutralize ——– and ————– are a higher priority and supersede these ———-
- Backbone
- Hydrophobicity
- Parameters
What do most transmembrane proteins contain? Why?
Often contain Gly
* For helix-helix interactions
* As most transmembrane proteins span the membrane multiple times
